Collect much configuration data and record all changes in a logbook
System Configuration Collector collects and classifies most of your UNIX/Linux/BSD configuration data in flat files called snapshots. This unique concept allows changes in snapshots of consecutive runs to be detected. These changes are added to a logbook that is helpful for administrators during troubleshooting and for auditors during audits. Snapshot and logbook are also available in HTML format. All data can be send to an SCC server where a web interface provides access to summaries and supports comparing snapshots of different servers and searching of all data. A WMI based Windows client is also available.
Tools to Archive to CD/DVD and retrieve file from archive with archive tracking database backend. Tracks multiple copies of files across media, with options to dump and archive MySQL (Remote and local) databases and subversion repositories.
A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
GNU make compatible but reliable and simpler build tool
Makepp, a build program which has a number of features that allow for reliable builds and simpler build files, is a drop-in replacement for GNU make. It supports almost all of the syntax that GNU make supports, and can be used with makefiles produced by utilities such as automake. It is called makepp (or make++) because it was designed with special support for C++, which has since been extended to other languages like Swig or embedded SQL. Some features that makepp adds to make are: greatly improved handling of builds that involve multiple makefiles (recursive make is no longer necessary); automatic scanning for include files; rebuild triggered if build command changes; checksum-based signature methods for reliable builds, smart enough to ignore whitespace or comment changes; extensibility through Perl programming (within your makefile); repositories (automatically importing files from another tree); build caches (not recompiling identically what a user of the same cache already did
General Number Field Sieve implementation
Extrect selected entries from LDIF files like grep
ldif-extract is a small 'grep' like tool to extract and convert data from LDIF files. It could be used standalone or also in a pipe together with other tools like ldapsearch.
Convert environment variables between scripting languages
A unix perl script to convert environment variables between scripting languages. For example, convert csh setup script to bash or the other way around. Supports bash, csh, ksh, modulecmd, perl, plist, sh, tclsh, tcsh, vim, yaml, and zsh. Complements http://modules.sourceforge.net/
Perstem is a Persian (Farsi) stemmer, morphological analyzer, transliterator, and partial part-of-speech tagger. Inflexional morphemes are separated or removed from their stems. Perstem can also tokenize and transliterate between various character set encodings and romanizations.
ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
NOTE: The projects is now being developed here: https://github.com/eugmes/fntsample A program for making font samples that show Unicode coverage of the font and are similar in appearance to Unicode charts. Samples can be saved as PDF or PostScript files.
Algorithm Based Automatic Contiguation of Assembled sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.
Set of scripts, part of the official Samba project, able to manage POSIX accounts (users, groups, machines) for SAMBA, stored in a LDAP directory used as a (sort-of) SAM database. Edited by IDEALX in the OpenTrust suite (Cryptonit, IMC, IDX-PKI...)
Eukaryotic Genome Assembler
!!! NEW !!! 1/2017 - We now have a version optimized for running Human assemblies on AWS: https://sourceforge.net/projects/meraculous20/files/Meraculous-v184.108.40.206-smp_patch1-2-gcac7312.tar.gz/download ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Fast and memory-efficient k-mer counts - Efficient deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a robust pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a Grid Engine-type cluster or a standalone multi-core server. Manuscripts in submission: https://arxiv.org/abs/1703.09852 https://arxiv.org/abs/1608.01031
Phage_Finder is a heuristic computer program written in PERL that uses BLASTP data, HMM results, and tRNA/tmRNA information to find prophage regions in complete bacterial genome sequences.
A small collection of my unix scripts written for my personal utility.
These three tools build Checkpoint, Cisco ASA or Netscreen policys from logfiles. They write dbedit, access-list or set address, set service and set policy commands for the traffic seen in the logs, that can be cut and pasted into the firewalls. WOOT
Learn Linux sysadmin from Windows PC using this Debian Virtual Box
An Oracle Virtual Box image, packaged as an appliance to be downloaded and run anywhere. Created on 32-bit Windows XP & Oracle Virtual box 4.2.6. The VM is a Debian Squeeze 6.0.7 i386. md5sum: 85ab2066b7381af12b741a3d4dedf6c9 This file is to be specifically used along with this other great project: http://nixsrv.com/llthw There is a 64bit Debian image similar to mine in that link above. To benefit those like me who still have 32bit machines, I have created and uploaded this image. This is your fast track to getting up and running in no time. I hope it benefits people with 32bit machines who want to take advantage of the tutorial ASAP. If you found the image helpful, please leave a short note of appreciation (and a thanks to the tutorial maker). I would like that very much. Thanks and Ciao.
Perl Portable is the amazingly powerful Perl Scripting language made into a portable application for Windows (To PortableApps.com standards. :D)
genome-wide computational identification of phasiRNAs
Phase siRNAs (phasiRNAs) are a class of small RNAs, which triggered by miRNA-targeted cleavage and followed by DCL4-mediated production of small RNAs phased in 21-nt increments. Here, we introduce PhaseTank to systematically characterize 'miRNA → mRNA → tasiRNA → target genes' regulatory casacades in plants. With one command analysis, PhaseTank is an easy-to-use software for users.
The Sound Description Interchange Format (SDIF) is an established standard for the interchange of sound descriptions and analysis data. This project provides libraries, SDIF (in C) and Easdif (in C++), tools, and wrappers to read and write SDIF files.
List packages that have no dependencies (like deborphan)
rpmorphan finds "orphaned" packages on your system (packages which have no other packages depending on their installation). A console and graphical interface is provided. It is a clone of deborphan debian software. It provides also some others rpm tools (rpmusage, rpmdep, rpmduplicates, rpmextra)
Auto SQL Injection Tool Coded by MR.SE
SQLInjection is one of the basics of hacking. It is also one of the most tedious and most time consuming steps. MR.SE SQL Injection Tool programmed under Perl and hackers can quickly and easily penetrate their desired website databases with this.
FireEgl's PuTTY -- FuTTY!
FuTTY is a fork of PuTTY and PuTTYTray.
ldap-searchEntries.pl is a small perl script that searches for entries based on a list provided by STDIN. The values given from STDIN are parsed into a filterstring containing placeholders. The found DNs are printed to STDOUT for each search. Parameters allow fine tuning of all features including attribute printing.
The repository of the binaries for Windows of Parrot (Perl6 VM). The Parrot speaks your language but lives on http://www.parrot.org/